Mercurial > repos > bgruening > vpt_segment

annotate macros.xml @ 3:0811613196a2 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1180d1e85b63beb3d2e7fd6e9c73b054a9348e7f
author bgruening
date Mon, 11 Aug 2025 08:53:09 +0000
parents a88a1e78702e
children
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5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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1 <macros>
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2 <token name="@TOOL_VERSION@">1.3.0</token>
3
0811613196a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1180d1e85b63beb3d2e7fd6e9c73b054a9348e7f
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3 <token name="@VERSION_SUFFIX@">3</token>
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4 <token name="@PROFILE@">23.0</token>
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5 <xml name="requirements">
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6 <requirements>
3
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7 <container type="docker">quay.io/bgruening/vpt:1.3.0-2</container>
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8 <yield/>
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9 </requirements>
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10 </xml>
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11 <xml name="creator">
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12 <creator>
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13 <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" />
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14 <person givenName="Amirhossein" familyName="Naghsh Nilchi" email="nilchia@informatik.uni-freiburg.de" />
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15 <person givenName="Pavan" familyName="Videm" email="videmp@informatik.uni-freiburg.de" />
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16 <person givenName="Björn" familyName="Grüning" email="gruening@informatik.uni-freiburg.de" />
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17 </creator>
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18 </xml>
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19 <token name="@CMD@"><![CDATA[
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20 mkdir -p 'input/images' 'input/model' 'output/' &&
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21 #for $image in $input_images:
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22 ln -s '$image' 'input/images/${image.element_identifier}.${image.ext}' &&
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23 #end for
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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24 ln -s '$input_micron_to_mosaic' 'input/micron_to_mosaic_pixel_transform.csv' &&
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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25 ]]></token>
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26 <token name="@COMMON_ARGS@"><![CDATA[
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27 --processes \${GALAXY_SLOTS:-10}
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28 --log-file 'output/log'
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29 ]]>
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30 </token>
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31 <xml name="common_input">
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32 <param argument="--input_images" type="data" format="tiff" multiple="true" label="MEROSCOPE tiff images"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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33 <param argument="--input_micron_to_mosaic" type="data" format="csv" label="Micron to mosaic mapping file"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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34 </xml>
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35 <xml name="normalization_param" token_label="Normalization">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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36 <param name="normalization" type="select" label="@LABEL@">
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37 <option value="default">default (min-max range normalization)</option>
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38 <option value="CLAHE">CLAHE (Contrast Limited Adaptive Histogram Equalization)</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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39 </param>
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40 </xml>
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41 <xml name="channel_options_basic">
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42 <yield/>
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43 <option value="Cellbound1">Cellbound1</option>
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44 <option value="Cellbound2">Cellbound2</option>
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45 <option value="Cellbound3">Cellbound3</option>
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46 </xml>
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47 <xml name="channel_options_none">
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48 <expand macro="channel_options_basic">
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49 <option value="None" selected="true">None</option>
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50 <option value="DAPI">DAPI</option>
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51 <option value="PolyT">PolyT</option>
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52 <yield/>
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53 </expand>
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54 </xml>
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55 <xml name="advanced_output">
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56 <section name="advanced_output" title="Advanced output options">
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57 <param name="log" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Output log?"/>
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58 </section>
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59 </xml>
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60 <xml name="common_output">
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61 <data name="vpt_log" format="txt" from_work_dir="output/log" label="${tool.name} on ${on_string}: VPT log">
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62 <filter>advanced_output['log']</filter>
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63 </data>
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64 </xml>
2
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65 <xml name="task_input_data">
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66 <conditional name="normalize_conditional">
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67 <param name="normalize_select" type="select" label="Perform Normalization?">
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68 <option value="Yes" selected="true">Yes</option>
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69 <option value="No">No</option>
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70 </param>
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71 <when value="Yes">
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72 <conditional name="normalize_type_conditional" label="Select normalization method">
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73 <expand macro="normalization_param"/>
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74 <when value="default"/>
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75 <when value="CLAHE">
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76 <param name="clip_limit" type="float" min="0" max="1" value="0.01" label="Clip limit" help="higher values give more contrast"/>
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77 <param name="filter_size" type="integer" min="1" value="100" label="Tile grid size"/>
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78 </when>
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79 </conditional>
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80 </when>
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81 <when value="No"/>
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82 </conditional>
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83 <conditional name="blur_conditional">
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84 <param name="blur_select" type="select" label="Perform Blur?">
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85 <option value="Yes">Yes</option>
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86 <option value="No" selected="true">No</option>
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87 </param>
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88 <when value="Yes">
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89 <param name="blur_options" type="select" label="Blur options">
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90 <option value="average">average</option>
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91 <option value="median">median</option>
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92 <option value="gaussian">gaussian</option>
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93 </param>
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94 <param name="kernel_size" type="integer" min="0" value="5" label="Kernel size in pixel"/>
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95 </when>
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96 <when value="No"/>
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97 </conditional>
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98 <conditional name="downsample_conditional">
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99 <param name="downsample_select" type="select" label="Perform downsample?">
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100 <option value="Yes">Yes</option>
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101 <option value="No" selected="true">No</option>
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102 </param>
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103 <when value="Yes">
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104 <param name="scale" type="float" min="0" value="2.0" label="Downsample" help="Reduces the size of the images during segmentation to decrease processing time" />
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105 </when>
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106 <when value="No"/>
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107 </conditional>
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108 </xml>
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109 <xml name="channel_map_conditional_childs">
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110 <when value="None"/>
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111 <when value="DAPI">
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112 <expand macro="task_input_data"/>
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113 </when>
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114 <when value="PolyT">
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115 <expand macro="task_input_data"/>
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116 </when>
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117 <when value="Cellbound1">
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118 <expand macro="task_input_data"/>
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119 </when>
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120 <when value="Cellbound2">
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121 <expand macro="task_input_data"/>
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122 </when>
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123 <when value="Cellbound3">
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124 <expand macro="task_input_data"/>
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125 </when>
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126 </xml>
0
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127 <xml name="sanitize_digits">
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128 <sanitizer invalid_char="">
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129 <valid initial="string.digits">
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130 <add value=","/>
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131 <add value="."/>
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132 </valid>
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133 </sanitizer>
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134 </xml>
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135 <xml name="citations">
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136 <citations>
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137 <citation type="bibtex">@Manual{github,
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138 title = {Vizgen Post-processing Tool},
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139 author = {Vizgen},
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140 organization = {Vizgen},
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141 year = {2022},
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142 url = {https://github.com/Vizgen/vizgen-postprocessing}}
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143 </citation>
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144 </citations>
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145 </xml>
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146 </macros>